Sam/paired processing (#120) (pinellolab#537)

* Implement crispresso_merge

* Add new crispresso_merge to args

* Update test_env.yml

* Parallel

* Fastq_out with single process only

* Native merge tests

* Remove unused aln_matrix

* Fix get consensus from pairs stubs

* Fix unit tests, upack 5 vasl

* Update score

* Update integration_tests.yml

* Update tests, remove insertions beyond amplicon

* Update tests, new score

* Update for deletions

* Update for deletions

* Update scores

* Update scores

* Update scores

* Fix fastq_output

* f-string fix

* CRISPResso_merge for core only

* Comments

* Unpin numpy<2

* Pin cython 3.0.12

* Pip install no isolation

* numpy fix

* Fix workflows

* Write and read slots during parallelization

* Delete unused test

* Add run native merge test to github actions

* Update c files with cython=3.1.0

* Remove import for ResultsSlotsDict

* Repoint tests at master

---------

Co-authored-by: Samuel Nichols <Snic9004@gmail.com>
Co-authored-by: mbowcut2 <mbowcut@gmail.com>

Author: 3 people

.github/envs/test_env.yml

@@ -14,5 +14,6 @@ dependencies:
   - scipy
   - matplotlib=3.8.4
   - pandas>2
+  - pytest-check
   - pip:
     - ydiff

.github/workflows/integration_tests.yml

@@ -79,6 +79,11 @@ jobs:
         run: |
           make prime-editor test print
 
+      - name: Run Native Merging
+        if: success() || failure()
+        run: |
+          make nhej_native_merge test print
+
       - name: Run BAM Input
         if: success() || failure()
         run: |